12 Works

Daphnia sinensis genome

Xiuping Zhang
The genomic mechanism by which aquatic organisms adapt to high-altitude environments remains unknown. In this study, we provide a high-quality chromosome-level genome assembly (~133 Mb, scaffold N50 11.3 Mb) of a water flea (Daphnia sinensis). This enabled us to discover that there have been chromosomal rearrangements between two subgenera of Daphnia. We further show that the D. sinensis population living on the Tibetan Plateau exhibits several key genomic adaptive features (e.g., enhanced expression of genes...

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae)

Diego F. Morales-Briones, Berit Gehrke, Chien-Hsun Huang, Aaron Liston, Hong Ma, Hannah Marx, David Tank & Ya Yang
Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. These approaches are prone...

Consistent pattern of higher lability of leaves from high latitudes for both native Phragmites australis and exotic Spartina alterniflora

Youzheng Zhang, Steven Pennings, Zixia Liu, Bo Li & Jihua Wu
1. Global variation in litter decomposition rates is driven by climate, decomposer taxa and litter quality. Most large-scale studies of litter quality have made comparisons across species, rather than within a species sourced from different latitudes. Here, we aim to explore latitudinal variation in leaf litter decomposition rate and litter quality within a species. 2. We investigated whether the typical interspecific pattern of increased litter lability at higher latitudes also holds within plant species, by...

Meta analysis data and fitness-related trait values

Zhiping Song
Crop-wild gene flow may alter the fitness performance of the recipient i.e. crop-wild hybrids, then potentially impact wild populations, especially for the gene flow carrying selective advantage crop alleles. Given the continuous crop-wild gene flow since crop domestication and the occasionally stressful environments, the extant wild populations of most crops are still "wild". This paradox hints some mechanisms may mitigate the effects of crop-wild gene flow but never been examined. We used wild rice (O....

Densities of mollusc species at different sites along the Chinese coast

He-Bo Peng, Ying-Chi Chan, Tanya Compton, Xue-Fei Cheng, David Melville, Shou-Dong Zhang, Zhengwang Zhang, Guangchun Lei, Zhijun Ma & Theunis Piersma
Aim: Molluscs are important grazers, filter and deposit feeders, scavengers and predators, which in turn are food for shorebirds, fish and people. Some species, targeted as human food, have been cultured along the Chinese coast for hundreds of years. To examine whether aquacultural practices have meanwhile affected biodiversity gradients, we measured mollusc community structure along the coast of China in habitats which are intensively used by humans. Location: Chinese coast Methods: We sampled 21 intertidal...

Genomic regions associated with adaptation to predation in Daphnia often include members of expanded gene families

Xiuping Zhang
Predation has been a major driver of the evolution of prey species, which consequently develop antipredator adaptations. However, little is known about the genetic basis underpinning the adaptation of prey to intensive predation. Here, we describe a high-quality chromosome-level genome assembly (approx. 145 Mb, scaffold N50 11.45 Mb) of Daphnia mitsukuri, a primary forage for many fish species. Transcriptional profiling of D. mitsukuri exposed to fish kairomone revealed that this cladoceran responds to predation risk...

Data from: Substantia nigra integrity correlates with sequential working memory in Parkinson’s disease

Zheng Ye, Lirong Jin, Thomas F. Muente, Wenyue Liu, Changpeng Wang, Tingting He, Minghong Su, Yuan Lu & Guanyu Zhang
Maintaining and manipulating sequential information online is essential for daily activities such as planning. In Parkinson’s disease (PD), deficits in sequential working memory have been associated with altered regional activation and functional connectivity within the basal ganglia. This study demonstrated that the substantia nigra (SN) integrity correlates with basal ganglia dysfunction during sequential working memory. We included 29 patients with PD and 29 healthy controls (HC). We assessed the SN integrity using neuromelanin-sensitive MRI and...

An invasive species erodes the performance of coastal wetland protected areas

Junlin Ren, Jianshe Chen, Changlin Xu, Johan Van De Koppel, Mads Thomsen, Shi-Yun Qiu, Fangyan Cheng, Wanjuan Song, Quan-Xing Liu, Chi Xu, Junhong Bai, Yihui Zhang, Baoshan Cui, Mark Bertness, Brian Silliman, Bo Li & Qiang He
The world has increasingly relied upon protected areas (PAs) to rescue highly valued ecosystems from human activities, but whether PAs will fare well with bioinvasions remains unknown. By analyzing three decades of seven largest coastal PAs in China, including multiple World Natural Heritage and/or Wetlands of International Importance sites, we show that although PAs are achieving success in rescuing iconic wetlands and critical shorebird habitats from once widespread reclamation, this success is counteracted by escalating...

Far Eastern Curlew and Whimbrel prefer flying low: wind support and good visibility appear only secondary factors in determining migratory flight altitude

Batbayar Galtbalt, Amanda Lilleyman, Jonathan T Coleman, Chuyu Cheng, Zhijun Ma, Danny I Rogers, Bradley K Woodworth, Richard A Fuller, Stephen T Garnett & Marcel Klaassen
Background: In-flight conditions are hypothesized to influence the timing and success of long-distance migration. Wind assistance and thermal uplift are thought to reduce the energetic costs of flight, humidity, air pressure and temperature may affect the migrants’ water balance, and clouds may impede navigation. Recent advances in animal-borne long-distance tracking enable evaluating the importance of these factors in determining animals’ flight altitude. Methods: Here we determine the effects of wind, humidity, temperature, cloud cover, and...

Land-use and elevation interact to shape bird functional and phylogenetic diversity and structure: Implications for designing optimal agriculture landscapes

Rachakonda Sreekar, Xingfeng Si, Katerina Sam, Jiajia Liu, Salindra Dayananda, Uromi Goodale, Sarath Kotagama & Eben Goodale
Conversion of rainforests into agriculture resulted in massive changes in species diversity and community structure. Although the conservation of the remaining rainforests is of utmost importance, identifying and creating biodiversity-friendly agriculture landscape is vital for preserving biodiversity and their functions. Biodiversity studies in agriculture have often been conducted at low elevations. In this study, we compared the functional diversity (FD), phylogenetic diversity (PD), and community structure of birds along an interacting gradient of land-use (protected...

Plant genotypic diversity effects on soil nematodes vary with trophic level

Jihua Wu, Jun Yan, Youzheng Zhang, Kerri M. Crawford, Xiaoyong Chen & Shuo Yu
At local spatial scales, loss of genetic diversity within species can lead to species loss. Few studies, however, have examined plant genotypic diversity effects across trophic levels. We investigated genotypic diversity effects of Phragmites australis on belowground biomass and soil nematode communities. Our results revealed belowground plant biomass and nematode abundance responses to plant genotypic diversity were uncoupled. Decreasing plant genotypic diversity decreased the abundance of lower, but not higher trophic level nematodes. Low plant...

Asynchrony among species and functional groups and temporal stability under perturbations: Patterns and consequences

Shurong Zhou
1. A number of theoretical and empirical studies have demonstrated effects of perturbations on ecosystem stability. Compensatory dynamics among taxonomic units have been proposed as a major mechanism regulating the temporal stability of biomass production (hereafter “temporal stability”). However, most studies have focused on the effects of species asynchrony on temporal stability in response to perturbations, and few studies examined how compensatory changes among functional groups affected temporal stability. 2. Here, we conducted a 4-year...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Fudan University
  • East China Normal University
  • Royal Netherlands Institute for Sea Research
  • Beijing Normal University
  • Chinese Academy of Sciences
  • University of Houston
  • Xiamen University
  • Duke University
  • University of Queensland
  • University of Lübeck